Musharraf, who ruled Pakistan for nine years after seizing power in a bloodless coup in 1999, returned to Pakistan from four years in self-imposed exile on March 24, vowing to run for the May 11 poll in four constituencies.
In the far northern town of Chitral, close to the Afghan border, officials approved Musharraf's candidature on Sunday.
"His papers are in order. He is not convicted so far, so we cannot disqualify him," returning officer Jamal Khan said.
But in the retired general's home city of Karachi, officials turned down his nomination on charges of violating the constitution and sacking top judges craft storage boxes
Returning officer Ikramur Rehman upheld objections raised by his rivals that Musharraf had violated the constitution and sacked top judges by imposing emergency rule in 2007.
"This is a biased decision," his party official Afzal Agha said, adding an appeal would be filed against rejection of Musharraf's nomination.
Musharraf's nomination papers were rejected in the Punjab town of Kasur on Friday and a decision on his bid to contest a seat in Islamabad is expected late on Sunday.
His powerbase has shrivelled since he stepped down after nine years of military rule in 2008 and faces a barrage of legal challenges dentist central
He has been granted bail over the 2007 killing of former prime minister Benazir Bhutto and a Baluch rebel leader in 2006, and for sacking and arresting judges in November 2007.
On Monday, the Supreme Court will hear a petition asking for Musharraf to be put on trial for treason for imposing emergency rule in 2007, a move that ultimately paved the way for his downfall yahoo seo hk